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1.7 Summary of Section 1

  1. Protein structure is described in terms of four levels of organisation: primary, secondary, tertiary and quaternary.

  2. The primary structure of a protein is the sequence of amino acids of which it is composed and ultimately determines the shape that the protein adopts.

  3. The peptide group formed between two amino acid residues has a rigid planar structure and these planar groups can rotate around the Cα–N and Cα–C bonds. In a polypeptide, the angles of rotation about these bonds (ɸ and ψ respectively) specify the conformation of the backbone. A Ramachandran plot of ɸ versus ψ, based on ‘allowed’ and ‘outer limit’ distances for contact between atoms, identifies those conformations that are sterically favourable or unfavourable.

  4. A polypeptide will tend to fold in such a way as to give a conformation that minimises its free energy (i.e. the most stable conformation).

  5. Secondary structure refers to the conformation adopted by the polypeptide backbone of a protein and includes helices, pleated sheets and turns. Secondary structures are stabilised by non-covalent interactions between atoms and groups in the polypeptide, namely hydrogen bonds and van der Waals attractions. Supersecondary structures or motifs are particular arrangements and combinations of two or three secondary structures, often with defined topology and three-dimensional structure.

  6. Tertiary structure describes how the polypeptide folds as a whole. There are certain distinct folding patterns common to many different proteins. Discrete independently folded structures within a single polypeptide are called domains. Domains are compact and stable, with a hydrophobic core, and frequently have distinct functions.

  7. Quaternary structure applies only to those proteins that consist of more than one polypeptide chain (subunit) and describes how subunits associate with each other.


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